md-mcp

Transform from Prompt Engineering to Context Engineering.

A lightweight Python library that instantly exposes your local markdown documentation, notes, and knowledge bases to any AI tool that supports the Model Context Protocol (MCP) – including Claude Desktop.

No embeddings, no preprocessing, and no uploading. Your files stay safely on your local machine, and any real-time updates are instantly reflected in your AI's context.

🚀 Quick Start

1. Install

Option A: Install from pypi

pip install md-mcp

Option B: Install from source code

uv sync

2. Launch the Web UI (Recommended)

The easiest way to manage your markdown servers is through the visual dashboard:

md-mcp --web

If the command is not recognized (e.g., if the Python scripts directory is not in your system PATH), you can run:

uv run python -m md_mcp --web

Just point at a folder and go!

3. Or use the CLI

If you prefer the command line:

# Expose a folder of markdown files
md-mcp --folder ~/Documents/notes --name "My Notes"

# That's it! Restart Claude Desktop and it's available.

Related MCP server: MCP Documentation Service

📋 Features

• Context Engineering: Feed your AI assistant exactly the right local context to get better answers, eliminating the need to endlessly prompt.

• Universal MCP Support: Works natively with Claude Desktop and any other AI tool or agent that supports the Model Context Protocol.

• Local & Secure First: Your files never leave your machine. No cloud uploads, no third-party APIs parsing your sensitive notes.

• Real-time Sync: Edit your markdown files and the MCP server picks up the changes instantly. No need to regenerate embeddings or re-index.

• Auto File Watching: Automatically detects when files are added, modified, or deleted (powered by watchdog). Use the rescan_folder() tool in Claude Desktop for manual refresh if needed.

• Zero Configuration: Just point at a folder and go.

• Auto-Discovery: Recursively finds all .md files.

• Metadata Extraction: Parses YAML frontmatter and first paragraphs for rich resource descriptions.

• Search Support: Built-in search across all files to quickly find the needle in the haystack.

• Web Interface: Easy-to-use visual dashboard for non-technical users to manage multiple knowledge bases.

• Observable by Default: Optional OpenTelemetry instrumentation (uv pip install "md-mcp[observability]") traces every MCP tool call — an audit trail of what your AI assistant actually did with your notes. See docker/README.md.

🎯 Use Cases

1. Personal Knowledge Base

md-mcp --folder ~/obsidian-vault --name "Obsidian"

→ Claude can now read your entire Obsidian vault

2. Project Documentation

md-mcp --folder ~/code/myproject/docs --name "Project Docs"

→ Claude has full context on your project

3. Research Papers

md-mcp --folder ~/research/papers-md --name "Research"

→ Claude can reference your research notes

📖 Advanced Usage commands

Web Interface (easiest way to use)

# Direct command (if in PATH)
md-mcp --web

# Or via Python module
uv run python -m md_mcp --web

# You can optionally specify a custom port (default is 5000)
md-mcp --web --port 8080
# or: uv run python -m md_mcp --web --port 8080

Add a Markdown Folder

# With explicit name
md-mcp --folder /path/to/docs --name "My Docs"

# Auto-name from folder
md-mcp --folder ~/notes
# Creates server named "notes"

# Alias: --add
md-mcp --add ~/work-docs --name "Work"

Scan Before Adding (Dry Run)

md-mcp --folder ~/notes --scan
# Shows what files would be exposed

List Configured Servers

md-mcp --list
# Shows all md-mcp servers

Show Configuration Status

md-mcp --status
# Shows Claude config path and all servers

Remove a Server

md-mcp --remove "My Docs"

Interactive Mode

md-mcp
# Prompts for folder path

🔧 How It Works

1. You run the CLI:

   md-mcp --folder ~/notes --name "Notes"

2. md-mcp:

   • Scans folder for .md files

   • Extracts metadata (frontmatter, descriptions)

   • Updates Claude Desktop config

   • Registers MCP server entry

3. In Claude Desktop:

   • Restart Claude

   • Server appears in MCP dropdown

   • All markdown files available as resources

   • Use search tools to find content

📂 What Gets Exposed

Each markdown file becomes an MCP Resource:

{
  "uri": "md://notes/project-plan.md",
  "name": "Project Plan",
  "description": "Auto-extracted from frontmatter or first paragraph",
  "mimeType": "text/markdown"
}

🛠️ MCP Tools

md-mcp provides three tools to Claude:

1. search_markdown

Search across all markdown files by content or filename.

Usage in Claude:

• Standard (keyword): > "Search my notes for 'docker compose'"

⚠️ Experimental features below: (may not work)

• Semantic: > "Search my docs for 'user authentication' using semantic search" (Finds related concepts like login, OAuth, etc.)

• Hybrid: > "Search for 'docker setup' using hybrid search" (Combines exact matching and conceptual matching)

(Note: Semantic and hybrid search require uv pip install "md-mcp[semantic]", or installing with the extra flag)

2. list_files

List all available markdown files.

Usage in Claude:

"What markdown files do I have about Python?"

3. rescan_folder

Manually rescan the folder for new, modified, or deleted markdown files. Use this if the automatic file watcher is not available or if files are missing.

Usage in Claude:

"Rescan the markdown folder to find my new notes"

📋 Requirements

• Python 3.10+

• mcp library

• Claude Desktop

🔧 Configuration

Claude Desktop Config Location (Automatic)

Windows: %APPDATA%\Claude\claude_desktop_config.json

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json

Linux: ~/.config/Claude/claude_desktop_config.json

Antigravity Config Location (Manual)

Windows: %USERPROFILE%\.gemini\antigravity\mcp_config.json

Add your config and run Developer: Reload Window from the Command Palette (Ctrl+Shift+P).

Config Entry Format

# With uv installed
{
  "mcpServers": {
    "my-notes": {
      "command": "uvx",
      "args": [
        "md-mcp",
        "--folder", "C:\\Users\\Yang\\notes",
        "--name", "my-notes"
      ]
    }
  }
}

# Without uv installed
{
  "mcpServers": {
    "my-notes": {
      "command": "python",
      "args": [
        "-m", "md_mcp.server_runner",
        "--folder", "C:\\Users\\Yang\\notes",
        "--name", "my-notes"
      ]
    }
  }
}

VS Code MCP Config (Manual)

For workspace-level tools, use a file at .vscode/mcp.json. See official VS Code MCP documentation.

Example .vscode/mcp.json:

{
  "servers": {
    "my-notes": {
      "command": "uvx",
      "args": [
        "md-mcp",
        "--folder", "C:\\Users\\Yang\\notes",
        "--name", "my-notes"
      ]
    }
  }
}

Sample Prompts to Test

Once configured, try these prompts with your AI assistant:

• "Search my-notes for 'Docker'"

• "List markdown files in my-notes"

• "What do my notes say about the system architecture?"

🧪 Testing

Test the Scanner

from md_mcp.scanner import MarkdownScanner

scanner = MarkdownScanner("~/notes")
files = scanner.scan()

for f in files:
    print(f"{f.name}: {f.description}")

Test the Server Locally

# Run server directly (stdio mode)
uv run python -m md_mcp.server_runner --folder ~/notes --name test

# Server listens on stdin/stdout for MCP protocol

📝 Markdown Frontmatter Support

md-mcp extracts metadata from YAML frontmatter:

---
title: My Document
description: A brief overview of the document
tags: [project, planning]
---

# Content starts here

Extracted fields:

• description → Used as resource description

• Other fields stored in frontmatter dict

If no frontmatter, first paragraph is used as description.

🚧 Roadmap

• v0.3: Smart chunking for large files

• v0.4: Semantic search with embeddings

• v1.0: Use web UI for all operations

🐛 Troubleshooting

"Server not showing in Claude Desktop"

1. Check config was updated:

   md-mcp --status

2. Verify file exists:

   # Windows
   type %APPDATA%\Claude\claude_desktop_config.json
   
   # Mac/Linux
   cat ~/.config/Claude/claude_desktop_config.json

3. Restart Claude Desktop completely

"No files found"

# Check what scanner finds
md-mcp --folder ~/notes --scan

"Permission denied"

Make sure the folder is readable:

# Check permissions
ls -la ~/notes

🏗️ Architecture

┌─────────────────┐
│  Claude Desktop │
│   (MCP Client)  │
└────────┬────────┘
         │ stdio (JSON-RPC)
         │
┌────────▼────────┐
│  md-mcp Server  │
│  (MCP Protocol) │
└────────┬────────┘
         │
┌────────▼────────┐
│ MarkdownScanner │
│  (File Reader)  │
└────────┬────────┘
         │
   ┌─────▼──────┐
   │ Filesystem │
   │  (*.md)    │
   └────────────┘

🤝 Comparison to Alternatives

📚 Development

Setup Dev Environment

git clone https://github.com/ly2xxx/md-mcp.git
cd md-mcp
uv sync --extra dev
#Equivalent to (pip install -e ".[dev]")

Run Tests

Run standard unit tests:

uv run pytest

Run AI Agent integration tests (BDD + DeepEval):

uv run deepeval test run sample-client/tests/step_defs/test_search_markdown.py

This project champions a new AI testing standard by combining Behavior-Driven Development (pytest-bdd) with LLM-as-a-judge metrics (DeepEval) to rigorously evaluate Agentic RAG workflows.

Format Code

uv run black md_mcp/

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Credits

Inspired by:

• Model Context Protocol by Anthropic

• netshare - File sharing tool by Yang Li

📮 Contact

Issues: https://github.com/ly2xxx/md-mcp/issues

Built by: Yang Li Date: 2026-02-16

🚀 Just point at a folder and go!